B-cell chronic lymphocytic leukemia (B-CLL) is one of the most common leukemias of the elderly. To date, although many prognostic factors are known, none are universal or easily accessible thus allowing for the stratification of patients to slow-go and aggressive-course groups. Recent studies have identified new recurrent mutations in CLL cells, including mutation of the gene encoding one of the spliceosome subunits, SF3B1, mutation or rearrangement of NOTCH1, a gene of well-known tumorigenesis association, and disruption of BIRC3, a member of the inhibitors of apoptosis (IAP) family. This article presents the current state-of-the-art findings concerning the prognostic significance of these new alterations, as well as an explanation of the mechanisms underlying their biological impact on CLL lymphocytes.